python3 -m jcvi.compara.catalog ortholog这步报错

[Sherry520]

您好，我分析共线性这步报错了

我的命令：

不带--no_strip_names的也试了，一样的错误。不设--cscore的也试了
python3 -m jcvi.compara.catalog ortholog Zm-CML103-REFERENCE-NAM-1-0 Zm-B97-REFERENCE-NAM-1-0 --cscore=.99 --no_strip_names

报错：

[06/14/24 10:55:50] DEBUG File Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.last found. Computation skipped. base.py:1382
DEBUG Assuming --qbed=Zm-CML103-REFERENCE-NAM-1-0.bed --sbed=Zm-B97-REFERENCE-NAM-1-0.bed synteny.py:390
DEBUG Load file Zm-CML103-REFERENCE-NAM-1-0.bed base.py:36
DEBUG Load file Zm-B97-REFERENCE-NAM-1-0.bed base.py:36
DEBUG Load BLAST file Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.last (total 5 lines) blastfilter.py:45
DEBUG Load file Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.last base.py:36
WARNING chr10_69353227-69357058:+ not in Zm-CML103-REFERENCE-NAM-1-0.bed blastfilter.py:64
WARNING chr10_69353227-69357058:+ not in Zm-CML103-REFERENCE-NAM-1-0.bed blastfilter.py:64
WARNING chr10_69353227-69357058:+ not in Zm-CML103-REFERENCE-NAM-1-0.bed blastfilter.py:64
WARNING chr10_69353227-69357058:+ not in Zm-CML103-REFERENCE-NAM-1-0.bed blastfilter.py:64
WARNING chr10_69353227-69357058:+ not in Zm-CML103-REFERENCE-NAM-1-0.bed blastfilter.py:64
DEBUG running the cscore filter (cscore>=0.99) .. blastfilter.py:107
DEBUG after filter (0->0) .. blastfilter.py:109
DEBUG running the local dups filter (tandem_Nmax=10) .. blastfilter.py:114
DEBUG after filter (0->0) .. blastfilter.py:154
DEBUG Assuming --qbed=Zm-CML103-REFERENCE-NAM-1-0.bed --sbed=Zm-B97-REFERENCE-NAM-1-0.bed synteny.py:390
DEBUG Load file Zm-CML103-REFERENCE-NAM-1-0.bed base.py:36
DEBUG Load file Zm-B97-REFERENCE-NAM-1-0.bed base.py:36
DEBUG Load file Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.last.filtered base.py:36
DEBUG A total of 0 BLAST imported from Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.last.filtered. synteny.py:277
DEBUG Chaining distance = 20 synteny.py:1794
DEBUG Load file Zm-CML103-REFERENCE-NAM-1-0.Zm-B97-REFERENCE-NAM-1-0.anchors base.py:36
DEBUG A total of 0 anchor was found. Aborted. synteny.py:1371
Traceback (most recent call last):
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 742, in ortholog
scan(dargs)
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/synteny.py", line 1811, in scan
summary([anchor_file])
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/synteny.py", line 1372, in summary
raise ValueError("A total of 0 anchor was found. Aborted.")
ValueError: A total of 0 anchor was found. Aborted.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/gyh/miniconda3/envs/jcvi/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/gyh/miniconda3/envs/jcvi/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 982, in
main()
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 88, in main
p.dispatch(globals())
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/apps/base.py", line 131, in dispatch
globalsaction
File "/home/gyh/.local/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 749, in ortholog
raise ValueError(e) from e
ValueError: A total of 0 anchor was found. Aborted.

这是我的bed文件

more Zm-CML103-REFERENCE-NAM-1-0.bed
chr10 69353226 69357058 Zm-CML103-REFERENCE-NAM-1-0 0 +

这是我的cds文件：

more Zm-CML103-REFERENCE-NAM-1-0.cds

[Sherry520]

cds的序列名字应该是什么格式才符合标准，我的cds文件是用seqkit工具从参考fa文件提取的；bed文件是0-base的，到了cds文件，起始坐标是应该比bed起始坐标加1

[tanghaibao]

@Sherry520

cds序列名称必须和 bed文件第四列出现的名字相匹配。
用你的例子，Zm-CML103-REFERENCE-NAM-1-0就可以了，不要前面的那一串。